Pre-rank genes based on expression data

Pre-rank genes based on expression data

Usage

RunGSEAPreRank(
  exprs,
  classes,
  case,
  control = NULL,
  method = c("signal_to_noise", "abs_signal_to_noise", "t_test", "ratio_of_classes",
    "diff_of_classes", "log2_ratio_of_classes", "s2n", "abs_s2n")
)

Arguments

exprs

Expression data matrix (genes x samples)

classes

A vector of class labels for each sample Must be in the same order as the columns of exprs

case

The case group name in the classes vector

control

The control group name in the classes vector If NULL, the control group will be the other groups in classes

method

The method to use for ranking One of "signal_to_noise", "abs_signal_to_noise", "t_test", "ratio_of_classes", "diff_of_classes", "log2_ratio_of_classes", "s2n", "abs_s2n"

Value

A vector of the rank values with names as the gene names

See also

https://gseapy.readthedocs.io/en/latest/run.html#gseapy.gsea